I have noticed the same problem. As late as today I needed to remove YAM because a script executed sunchronuosly by YAM hanged as it tried to access YAM which was sleeping waiting for the script
But even if I removed YAM, the commoditie, all ports associated and stuff I still could not start another copy of YAM.
I think muimaster.library has an internal list of all programs started so it will always know if a program has been started even if everything else is removed. Even the commoditie, which normally is used to achieve this single mode causing the "Could not create applicating (because another one is already running)" message is not enought to be removed but muimaster needs to be removed. This means that you will have to close all MUI programs (which is alot of work, atleast for me; AmIRC, YAM, IBrowse, DagensTV, Onyx Prelude, Miami(!!), AmiStart and DRemind always running in the background).
This is what I think....
